working, refactoring for multi scene set vegetation

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

@@ -6235,7 +6235,7 @@ if (MORE_BUTTONS) {
 				return;
 			}
 			   if ((images[0].getProperty("timestamp")==null) || (((String) images[0].getProperty("timestamp")).length()==0)) {
-				   (new JP46_Reader_camera(false)).decodeProperiesFromInfo(images[0]);
+				   JP46_Reader_camera.decodeProperiesFromInfo(images[0]);
 			   }
 
 			if (GONIOMETER==null) {
@@ -10880,7 +10880,7 @@ if (MORE_BUTTONS) {
             		}
             	}
             	imp_sel=new ImagePlus(sourceFilesList[numFile]); // read source file
-            	JP4_INSTANCE.decodeProperiesFromInfo(imp_sel);
+            	JP46_Reader_camera.decodeProperiesFromInfo(imp_sel);
 //            	matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.FFTSize); // TODO: is it needed each time?
 				int sensor_type = 0; // EO
 				matchSimulatedPattern= new MatchSimulatedPattern(DISTORTION.getFFTSize(sensor_type));
@@ -12204,7 +12204,7 @@ if (MORE_BUTTONS) {
 		imp.setProperty("motor1", ""+focusMeasurementParameters.motorPos[0]);
 		imp.setProperty("motor2", ""+focusMeasurementParameters.motorPos[1]);
 		imp.setProperty("motor3", ""+focusMeasurementParameters.motorPos[2]);
-    	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+    	JP46_Reader_camera.encodeProperiesToInfo(imp);
 		if (alwaysShow || focusMeasurementParameters.showResults) imp.show();
 		if (alwaysSave || focusMeasurementParameters.saveResults) {
 			String dir=getResultsPath(focusMeasurementParameters);
@@ -14137,7 +14137,7 @@ if (MORE_BUTTONS) {
 					}
 				}
 			}
-	    	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_psf);
+	    	JP46_Reader_camera.encodeProperiesToInfo(imp_psf);
 			if (showPSF) imp_psf.show();
 			if (focusMeasurementParameters.saveResults) {
 				String dir=getResultsPath(focusMeasurementParameters);

src/main/java/com/elphel/imagej/calibration/DistortionCalibrationData.java

@@ -3435,16 +3435,16 @@ import ij.text.TextWindow;
         	return null;
         }
 
-        public double getImageTimestamp(ImagePlus image){
+        public static double getImageTimestamp(ImagePlus image){
         	if ((image.getProperty("timestamp")==null) || (((String) image.getProperty("timestamp")).length()==0)) {
-        		(new JP46_Reader_camera(false)).decodeProperiesFromInfo(image);
+        		JP46_Reader_camera.decodeProperiesFromInfo(image);
         	}
         	return Double.parseDouble((String) image.getProperty("timestamp"));
         }
 
         public int getImageChannel(ImagePlus image){
         	if ((image.getProperty("channel")==null) || (((String) image.getProperty("channel")).length()==0)) {
-        		(new JP46_Reader_camera(false)).decodeProperiesFromInfo(image);
+        		JP46_Reader_camera.decodeProperiesFromInfo(image);
         	}
 
         	String channelSuffix=(String) image.getProperty("channel");
@@ -4462,7 +4462,7 @@ import ij.text.TextWindow;
         	// read image info to properties (if it was not done yet - should it?
         	if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) {
         		JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-        		jp4_instance.decodeProperiesFromInfo(imp);
+        		JP46_Reader_camera.decodeProperiesFromInfo(imp);
         	}
         	int [] motorPos=new int [numMotors];
         	int numMotorsDetected=0;
@@ -4481,7 +4481,7 @@ import ij.text.TextWindow;
         	// read image info to properties (if it was not done yet - should it?
         	if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) {
         		JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-        		jp4_instance.decodeProperiesFromInfo(imp);
+        		JP46_Reader_camera.decodeProperiesFromInfo(imp);
         	}
         	if (imp.getProperty("USED_POINTERS")!=null) {
         		return Integer.parseInt((String) imp.getProperty("USED_POINTERS"));
@@ -4984,7 +4984,7 @@ import ij.text.TextWindow;
         		IJ.showMessage("Error",msg);
         		throw new IllegalArgumentException (msg);
         	}
-        	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+        	JP46_Reader_camera.decodeProperiesFromInfo(imp);
         	if (imp.getProperty("shrinkGridForMask")!=null)
         		eyesisCameraParameters.shrinkGridForMask=Integer.parseInt((String) imp.getProperty("shrinkGridForMask"));
             	if (imp.getProperty("maskBlurSigma")!=null)
@@ -5116,7 +5116,7 @@ import ij.text.TextWindow;
         	imp.setProperty("maskBlurSigma", ""+eyesisCameraParameters.maskBlurSigma);
         	imp.setProperty("decimateMasks", ""+eyesisCameraParameters.getDecimateMasks());
 
-        	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+        	JP46_Reader_camera.encodeProperiesToInfo(imp);
         	imp.getProcessor().resetMinAndMax();
         	return imp;
         }

src/main/java/com/elphel/imagej/calibration/Distortions.java

@@ -3784,7 +3784,7 @@ For each point in the image
 			if (grid_path != null) {
 				ImagePlus imp = new ImagePlus(grid_path);
 				JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-				jp4_instance.decodeProperiesFromInfo(imp);
+				JP46_Reader_camera.decodeProperiesFromInfo(imp);
 				MatchSimulatedPattern.setPointersXYUV(imp, xyuv);
 				updateGridToPointer(imp, xyuv);
 				jp4_instance.encodeProperiesToInfo(imp);
@@ -7237,7 +7237,7 @@ List calibration
        	}
 
     	//camerasInterface, numSensor
-    	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+    	JP46_Reader_camera.encodeProperiesToInfo(imp);
     	imp.getProcessor().resetMinAndMax();
     	return imp;
     }
@@ -7291,7 +7291,7 @@ List calibration
     		throw new IllegalArgumentException (msg);
     	}
     	if (this.debugLevel>0) System.out.println("Read "+path+" as a sensor calibration data");
-    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+    	JP46_Reader_camera.decodeProperiesFromInfo(imp);
     	setDistortionFromImageStack(distortionCalibrationData,
     			imp,
     			numSensor,

src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java

@@ -130,7 +130,7 @@ public class EyesisAberrations {
 
    			ImagePlus impInvertedPSF = new ImagePlus("interpolated kernel stack", stack);
    			JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-   			jp4_instance.decodeProperiesFromInfo(impSpsf);
+   			JP46_Reader_camera.decodeProperiesFromInfo(impSpsf);
    			// copy properties from the source image
    			jp4_instance.copyProperties (impSpsf,impInvertedPSF);
    			inverseParameters.setProperties("INVERSE.", impInvertedPSF);
@@ -731,7 +731,7 @@ public class EyesisAberrations {
 
    			ImagePlus impInterpolatedPSF = new ImagePlus("interpolated kernel stack", stack);
    			JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-   			jp4_instance.decodeProperiesFromInfo(impSpsf);
+   			JP46_Reader_camera.decodeProperiesFromInfo(impSpsf);
    			// copy properties from the source image
    			jp4_instance.copyProperties (impSpsf,impInterpolatedPSF);
    			interpolateParameters.setProperties("INTERPOLATE.", impInterpolatedPSF);
@@ -1249,7 +1249,7 @@ public class EyesisAberrations {
     	for (int imgNum=0;imgNum<files.length;imgNum++){ // add stopRequested
 			if (debugLevel>0) System.out.println("Processing file #"+(imgNum+1)+ " ( of "+files.length+") :"+files[imgNum][0]);
         	ImagePlus imp=new ImagePlus(files[imgNum][0]); // read source file
-        	JP4_INSTANCE.decodeProperiesFromInfo(imp);
+        	JP46_Reader_camera.decodeProperiesFromInfo(imp);
 //       		boolean is_lwir =      lwirReaderParameters.is_LWIR(imp);
        		int sensor_type =      LwirReaderParameters.sensorType(imp);
 //       	    int     fft_size =     is_lwir ? distortionParameters.FFTSize_lwir :    distortionParameters.FFTSize;
@@ -1502,7 +1502,7 @@ public class EyesisAberrations {
 			// see if it has any usable properties and impProto is not set yet
 			if (impProtoIndex<0){
 				if ((imp_sel.getProperty("timestamp")==null) || (((String) imp_sel.getProperty("timestamp")).length()==0)) {
-					jp4_instance.decodeProperiesFromInfo(imp_sel);
+					JP46_Reader_camera.decodeProperiesFromInfo(imp_sel);
 					if ((imp_sel.getProperty("timestamp")!=null) && (((String) imp_sel.getProperty("timestamp")).length()>0)) {
 						impProtoIndex=nFile;
 					}
@@ -1867,7 +1867,7 @@ public class EyesisAberrations {
 
         if (impProtoIndex>=0){
 			imp_sel=opener.openImage("", filenames[impProtoIndex]);
-			jp4_instance.decodeProperiesFromInfo(imp_sel);
+			JP46_Reader_camera.decodeProperiesFromInfo(imp_sel);
 			// copy properties from the source image
 			jp4_instance.copyProperties (imp_sel,imp_psf);
         }
@@ -2167,7 +2167,7 @@ public class EyesisAberrations {
 
 		JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
 		if ((impSrc.getProperty("timestamp")==null) || (((String) impSrc.getProperty("timestamp")).length()==0)) {
-			jp4_instance.decodeProperiesFromInfo(impSrc);
+			JP46_Reader_camera.decodeProperiesFromInfo(impSrc);
 		}
 		// copy properies from the source image
 		jp4_instance.copyProperties (impSrc,impPsf);

src/main/java/com/elphel/imagej/calibration/Goniometer.java

@@ -633,7 +633,7 @@ horizontal axis:
 
 		
 //		int stationNumber= distortionCalibrationData.getImageStation(numGridImage), // station number
-		double timeStamp=  distortionCalibrationData.getImageTimestamp(images[nImg]);
+		double timeStamp=  DistortionCalibrationData.getImageTimestamp(images[nImg]);
 
 		int numPointers=pointersArray[nImg];
 		double [] goniometerTiltAxial=distortionCalibrationData.getImagesetTiltAxial(timeStamp);

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

@@ -7450,7 +7450,7 @@ public class MatchSimulatedPattern {
 		// read image info to properties (if it was not done yet - should it?
 		if ((imp.getProperty("timestamp") == null) || (((String) imp.getProperty("timestamp")).length() == 0)) {
 			JP46_Reader_camera jp4_instance = new JP46_Reader_camera(false);
-			jp4_instance.decodeProperiesFromInfo(imp);
+			JP46_Reader_camera.decodeProperiesFromInfo(imp);
 		}
 		double[][] pointersXY = new double[numPointers][];
 		int numPointerDetected = 0;
@@ -7477,7 +7477,7 @@ public class MatchSimulatedPattern {
 		// read image info to properties (if it was not done yet - should it?
 		if ((imp.getProperty("timestamp") == null) || (((String) imp.getProperty("timestamp")).length() == 0)) {
 			JP46_Reader_camera jp4_instance = new JP46_Reader_camera(false);
-			jp4_instance.decodeProperiesFromInfo(imp);
+			JP46_Reader_camera.decodeProperiesFromInfo(imp);
 		}
 		double[][] pointersXY = new double[numPointers][];
 		int numPointerDetected = 0;
@@ -7512,7 +7512,7 @@ public class MatchSimulatedPattern {
 	public static void setPointersXYUV(ImagePlus imp, double[][] pointersXYUV) {
 
 //		JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-//		jp4_instance.decodeProperiesFromInfo(imp);
+//		JP46_Reader_camera.decodeProperiesFromInfo(imp);
 		String prefix = "POINTER_";
 		Properties prop = imp.getProperties();
 		// Delete all properties starting with "POINTER_"
@@ -7547,7 +7547,7 @@ public class MatchSimulatedPattern {
 		// read image info to properties (if it was not done yet - should it?
 		if ((imp.getProperty("timestamp") == null) || (((String) imp.getProperty("timestamp")).length() == 0)) {
 			JP46_Reader_camera jp4_instance = new JP46_Reader_camera(false);
-			jp4_instance.decodeProperiesFromInfo(imp);
+			JP46_Reader_camera.decodeProperiesFromInfo(imp);
 		}
 		if (imp.getProperty("channel") == null)
 			return null;

src/main/java/com/elphel/imagej/calibration/PatternParameters.java

@@ -327,7 +327,7 @@ import ij.io.Opener;
         		IJ.showMessage("Error",msg);
         		throw new IllegalArgumentException (msg);
         	}
-        	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+        	JP46_Reader_camera.decodeProperiesFromInfo(imp);
         	setGridFromImageStack(imp);
         	this.pathName=path;
 			if (this.debugLevel>0) System.out.println("Opened "+path+" as a stack of the pattern grid geometry");
@@ -524,7 +524,7 @@ import ij.io.Opener;
         	imp.setProperty("AverageGreen", ""+this.averageRGB[1]);
         	imp.setProperty("AverageBlue",  ""+this.averageRGB[2]);
         	if (numZCorr>0) imp.setProperty("numZCorr",  ""+numZCorr);
-        	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+        	JP46_Reader_camera.encodeProperiesToInfo(imp);
         	imp.getProcessor().resetMinAndMax();
         	return imp;
         }

src/main/java/com/elphel/imagej/calibration/PixelMapping.java

@@ -463,7 +463,7 @@ public class PixelMapping {
     		IJ.showMessage("Error",msg);
     		throw new IllegalArgumentException (msg);
     	}
-    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+    	JP46_Reader_camera.decodeProperiesFromInfo(imp);
     	return resampleToEquirectangular(
         		imp,
         		channel,
@@ -666,7 +666,7 @@ public class PixelMapping {
 		impOut.setProperty("YPosition", ""+erm.mapWOI.y); // real XPosition as tiff tag 0x11f is rational (5)
 		impOut.setProperty("ImageFullWidth", "" +erm.pixelsHorizontal);// real ImageFullWidth as tiff tag 0x8214 is rational (5)
 		impOut.setProperty("ImageFullLength", ""+erm.pixelsVertical);   // real ImageFullLength as tiff tag 0x8215 is rational (5)
-		(new JP46_Reader_camera(false)).encodeProperiesToInfo(impOut);
+		JP46_Reader_camera.encodeProperiesToInfo(impOut);
 		impOut.getProcessor().resetMinAndMax();
 		return impOut;
     }
@@ -768,7 +768,7 @@ public class PixelMapping {
 		impOut.setProperty("YPosition", ""+erm.mapWOI.y); // real XPosition as tiff tag 0x11f is rational (5)
 		impOut.setProperty("ImageFullWidth", "" +erm.pixelsHorizontal);// real ImageFullWidth as tiff tag 0x8214 is rational (5)
 		impOut.setProperty("ImageFullLength", ""+erm.pixelsVertical);   // real ImageFullLength as tiff tag 0x8215 is rational (5)
-		(new JP46_Reader_camera(false)).encodeProperiesToInfo(impOut);
+		JP46_Reader_camera.encodeProperiesToInfo(impOut);
 		impOut.getProcessor().resetMinAndMax();
 		return impOut;
     }
@@ -1176,7 +1176,7 @@ public class PixelMapping {
     		throw new IllegalArgumentException (msg);
     	}
 		if (debugLevel>0) System.out.println("Read "+path+" as an inter-sensor overlap map");
-    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(impMap);
+    	JP46_Reader_camera.decodeProperiesFromInfo(impMap);
     	InterSensor interSensor=new InterSensor(impMap,debugLevel);
     	this.lastUsedInterSensor=interSensor;
     	double [][] aYCbCr=convertToDouble?(new double [8][]):null;
@@ -1263,7 +1263,7 @@ public class PixelMapping {
     		throw new IllegalArgumentException (msg);
     	}
 		if (debugLevel>0) System.out.println("Read "+path+" as a plane-to-sensor map");
-    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(impMap);
+    	JP46_Reader_camera.decodeProperiesFromInfo(impMap);
     	InterSensor interSensor=new InterSensor(impMap,debugLevel);
     	this.lastUsedInterSensor=interSensor;
     	for (int iChn=0;iChn<interSensor.channel.length;iChn++){
@@ -1684,7 +1684,7 @@ public class PixelMapping {
     	var dispScales_2_y = -0.2898449402;
 */
 
-    	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+    	JP46_Reader_camera.encodeProperiesToInfo(imp);
     	return imp;
     }
 
@@ -2046,7 +2046,7 @@ public class PixelMapping {
     	imp.setProperty("interVectorY",  ""+vectors[1][1]);
     	imp.setProperty("interVectorZ",  ""+vectors[1][2]);
 
-    	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+    	JP46_Reader_camera.encodeProperiesToInfo(imp);
     	return imp;
     }
 
@@ -2424,7 +2424,7 @@ public class PixelMapping {
     		String [] requiredProperties=generateRequiredProperties(this.numOverlapChannels);
 
     		// try to decode info if required properties are not set
-    		if (imp.getProperty(requiredProperties[0])==null) (new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+    		if (imp.getProperty(requiredProperties[0])==null) JP46_Reader_camera.decodeProperiesFromInfo(imp);
 
     		for (int i=0; i<requiredProperties.length;i++) if (imp.getProperty(requiredProperties[i])==null){
     			String msg="Required property "+requiredProperties[i]+" is not defined in "+imp.getTitle();
@@ -5196,7 +5196,7 @@ public class PixelMapping {
                     	imp_stack.setProperty("disparityScalesY_"+i, this.disparityScales[i][1]+"");
                     }
       			}
-               	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_stack);
+               	JP46_Reader_camera.encodeProperiesToInfo(imp_stack);
         		imp_stack.getProcessor().resetMinAndMax();
         		if (show) imp_stack.show();
         		return imp_stack;
@@ -5211,7 +5211,7 @@ public class PixelMapping {
                 		"tilesY",
                 		"tilesX",
                 		"numPairs"};
-            	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+            	JP46_Reader_camera.decodeProperiesFromInfo(imp);
                 for (int i=0; i<requiredProperties.length;i++) if (imp.getProperty(requiredProperties[i])==null){
             		String msg="Required property "+requiredProperties[i]+" is not defined in "+imp.getTitle();
             		IJ.showMessage("Error",msg);
@@ -15675,7 +15675,7 @@ public class PixelMapping {
     		ImagePlus impOut=new ImagePlus(imageTitle,cp);
     		impOut.setProperty("channel",   ""+channel);  // image channel
     		for (int i=0;i<this.channel.length;i++) impOut.setProperty("channel"+(i+1),   ""+this.channel[i]);  // image channel
-    		(new JP46_Reader_camera(false)).encodeProperiesToInfo(impOut);
+    		JP46_Reader_camera.encodeProperiesToInfo(impOut);
     		impOut.getProcessor().resetMinAndMax();
     		return impOut;
     	}
@@ -16175,7 +16175,7 @@ public class PixelMapping {
 	        	imp.setProperty("latitudeTop",    ""+this.latitudeTop);
 	        	imp.setProperty("latitudeBottom", ""+this.latitudeBottom);
 
-	        	(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+	        	JP46_Reader_camera.encodeProperiesToInfo(imp);
 	        	imp.getProcessor().resetMinAndMax();
 	        	return imp;
 	        }
@@ -16188,7 +16188,7 @@ public class PixelMapping {
 	        		IJ.showMessage("Error",msg);
 	        		throw new IllegalArgumentException (msg);
 	        	}
-	        	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+	        	JP46_Reader_camera.decodeProperiesFromInfo(imp);
 	        	this.mapWOI=new Rectangle();
 	        	this.mapWOI.width=imp.getWidth();
 	        	this.mapWOI.height=imp.getHeight();
@@ -16292,7 +16292,7 @@ public class PixelMapping {
 	    		return;
 	    	}
 			if (this.debugLevel>1) System.out.println("Read "+path+" as a sensor calibration data");
-	    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+	    	JP46_Reader_camera.decodeProperiesFromInfo(imp);
 	    	setSensorDataFromImageStack(imp);
 	    }
 	    public SensorData (){} // just to get parameter names

src/main/java/com/elphel/imagej/calibration/hardware/CamerasInterface.java

@@ -1565,7 +1565,7 @@ public class CamerasInterface{
 	   							if (debugLevel>2) jp4_Instance.encodeProperiesToInfo(images[imageIndex]);
 	   							if (debugLevel>2) {
 	   								jp4_Instance.listImageProperties(images[imageIndex]);
-	   								jp4_Instance.decodeProperiesFromInfo(images[imageIndex]);
+	   								JP46_Reader_camera.decodeProperiesFromInfo(images[imageIndex]);
 	   								jp4_Instance.listImageProperties(images[imageIndex]);
 	   							}
 	   							String title=IJ.d2s(timestamps[iIP],6).replace('.','_')+String.format("-%02d.tiff", imageIndex); // sensor number

src/main/java/com/elphel/imagej/cameras/SFEPhases.java

@@ -741,7 +741,7 @@ public class SFEPhases {
 		// read image info to properties (if it was not done yet - should it?
 		if ((imp.getProperty("timestamp")==null) || (((String) imp.getProperty("timestamp")).length()==0)) {
 			JP46_Reader_camera jp4_instance= new JP46_Reader_camera(false);
-			jp4_instance.decodeProperiesFromInfo(imp);
+			JP46_Reader_camera.decodeProperiesFromInfo(imp);
 		}
 		if (imp.getProperty("channel")==null) return null;
 		return (String) imp.getProperty("channel");
@@ -1106,7 +1106,7 @@ public class SFEPhases {
     		throw new IllegalArgumentException (msg);
     	}
 		if (this.debugLevel>0) System.out.println("Read "+path+" as a sensor calibration data");
-    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp);
+    	JP46_Reader_camera.decodeProperiesFromInfo(imp);
     	setDistortionFromImageStack(imp, numSensor, overwriteExtrinsic);
  * 
  D5917: public void setDistortionFromImageStack(String path, boolean overwriteExtrinsic){

src/main/java/com/elphel/imagej/correction/Aberration_Correction.java

@@ -1614,7 +1614,7 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
 		        		IJ.showMessage("Error",msg);
 		        		throw new IllegalArgumentException (msg);
 		        	}
-		        	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_composite);
+		        	JP46_Reader_camera.decodeProperiesFromInfo(imp_composite);
 		        	imp_composite.setProperty("isTiff", true);
 			  } else {
 				  imp_composite=JP4_instance.open(

src/main/java/com/elphel/imagej/correction/EyesisCorrections.java

@@ -334,8 +334,8 @@ public class EyesisCorrections {
 							false); // do not show
 				} else {
 					imp=new ImagePlus(paths[nFile]);
-					//				  (new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_src); // decode existent properties from info
-					JP4_INSTANCE.decodeProperiesFromInfo(imp); // decode existent properties from info
+					//				  JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
+					JP46_Reader_camera.decodeProperiesFromInfo(imp); // decode existent properties from info
 				}
 				 */
 				if ((imp != null) &&(imp.getProperty("EXPOSURE")!=null)){
@@ -883,8 +883,8 @@ public class EyesisCorrections {
 				// do we need to add any properties?
 			} else {
 				imp_src=new ImagePlus(sourceFiles[nFile]);
-				//				  (new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_src); // decode existent properties from info
-				JP4_INSTANCE.decodeProperiesFromInfo(imp_src); // decode existent properties from info
+				//				  JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
+				JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
 				if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
 			}
 			double scaleExposure=1.0;
@@ -1005,7 +1005,7 @@ public class EyesisCorrections {
 		}
 		(new JP46_Reader_camera(false)).copyProperties (imp, imp_croped);
 		if (right) imp_croped.setProperty("XPosition", "0");
-		(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_croped);
+		JP46_Reader_camera.encodeProperiesToInfo(imp_croped);
 		return imp_croped;
 	}
 

src/main/java/com/elphel/imagej/correction/EyesisDCT.java

@@ -31,6 +31,7 @@ import com.elphel.imagej.cameras.EyesisCorrectionParameters;
 import com.elphel.imagej.common.DoubleGaussianBlur;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.dct.FactorConvKernel;
+import com.elphel.imagej.jp4.JP46_Reader_camera;
 import com.elphel.imagej.tileprocessor.DttRad2;
 import com.elphel.imagej.tileprocessor.ImageDtt;
 
@@ -1016,8 +1017,8 @@ public class EyesisDCT {
 				  // do we need to add any properties?
 			  } else {
 				  imp_src=new ImagePlus(sourceFiles[nFile]);
-				  //					  (new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_src); // decode existent properties from info
-				  eyesisCorrections.JP4_INSTANCE.decodeProperiesFromInfo(imp_src); // decode existent properties from info
+				  //					  JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
+				  JP46_Reader_camera.decodeProperiesFromInfo(imp_src); // decode existent properties from info
 				  if (debugLevel>0) System.out.println("Processing "+sourceFiles[nFile]);
 			  }
 			  double scaleExposure=1.0;

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -868,6 +868,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Test Orange", panelOrange, color_process);
 			addButton("Process Merged", panelOrange, color_process);
 			addButton("Vegetation LMA", panelOrange, color_process);
+			addButton("Combine LMA Segments", panelOrange, color_process);
 			plugInFrame.add(panelOrange);
 		}
 		plugInFrame.pack();
@@ -5604,7 +5605,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				IJ.showMessage("Error", "There are no images open\nProcess canceled");
 				return;
 			}
-			(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_sel);
+			JP46_Reader_camera.decodeProperiesFromInfo(imp_sel);
 			ArrayList<String> prop_kv = new ArrayList<String>();
 			Set<Object> jp4_set;
 			Properties jp4_prop;
@@ -5660,7 +5661,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					imp_sel.setProperty(name, val);
 				}
 			}
-			(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_sel);
+			JP46_Reader_camera.encodeProperiesToInfo(imp_sel);
 			return;
 		} else if (label.equals("Build World")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
@@ -5801,7 +5802,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		} else if (label.equals("Process Merged")) {
 			OrangeTest.processMerged();			
 		} else if (label.equals("Vegetation LMA")) {
-			VegetationModel.testVegetationLMA();			
+			VegetationModel.testVegetationLMA(false); //boolean combine_segments);			
+		} else if (label.equals("Combine LMA Segments")) {
+			VegetationModel.testVegetationLMA(true); //boolean combine_segments);			
 		}
 		//
 	}
@@ -10279,7 +10282,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 								IJ.showMessage("Error", msg);
 								throw new IllegalArgumentException(msg);
 							}
-							(new JP46_Reader_camera(false)).decodeProperiesFromInfo(imp_composite);
+							JP46_Reader_camera.decodeProperiesFromInfo(imp_composite);
 							imp_composite.setProperty("isTiff", true);
 						} else {
 							imp_composite = JP4_instance.open(directories[nFile], // path,

src/main/java/com/elphel/imagej/correction/PostProcessing.java

@@ -96,7 +96,7 @@ public class PostProcessing {
     		throw new IllegalArgumentException (msg);
     	}
 		if (debugLevel>0) System.out.println("Read "+mapsPath+" as an inter-sensor overlap map");
-    	(new JP46_Reader_camera(false)).decodeProperiesFromInfo(impMap);
+    	JP46_Reader_camera.decodeProperiesFromInfo(impMap);
     	this.interSensor=pixelMapping.new InterSensor(impMap,debugLevel);
 		System.out.println("Converting source files");
 		this.debugLevel= debugLevel;

src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java

@@ -1451,7 +1451,7 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 	}
 
 
-	public ImagePlus encodeProperiesToInfo(ImagePlus imp){
+	public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
 		String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
 		Set<Object> jp4_set;
 		Properties jp4_prop;
@@ -1471,7 +1471,7 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 		imp.setProperty("Info", info);
 		return imp;
 	}
-	public boolean decodeProperiesFromInfo(ImagePlus imp){
+	public static boolean decodeProperiesFromInfo(ImagePlus imp){
 		if (imp.getProperty("Info")==null) return false;
 		String xml= (String) imp.getProperty("Info");
 

src/main/java/com/elphel/imagej/tileprocessor/MLStats.java

@@ -427,7 +427,7 @@ public class MLStats {
 		imp.setProperty("disparity_outlier",  disparity_outlier+"");
 		imp.setProperty("comment_disparity_outlier",  "Ignore tiles with disparity difference higher");
 
-		(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp);
+		JP46_Reader_camera.encodeProperiesToInfo(imp);
 		imp.show();
 		return true;
 

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

@@ -10329,7 +10329,7 @@ public class OpticalFlow {
 			imp_ml.setProperty("metaFGDisparity",     ""+10); //=="metaGTDisparity"
 			imp_ml.setProperty("metaBGDisparityAll",  ""+11);
 			imp_ml.setProperty("metaBlueSky",         ""+12);
-			(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_ml);			
+			JP46_Reader_camera.encodeProperiesToInfo(imp_ml);			
 			FileSaver fs=new FileSaver(imp_ml);
 			fs.saveAsTiff(file_path);
 			System.out.println("intersceneExport(): saved "+file_path);
@@ -10474,7 +10474,7 @@ public class OpticalFlow {
 			imp_ml.setProperty("metaFGDisparity",     ""+10); //=="metaGTDisparity"
 			imp_ml.setProperty("metaBGDisparityAll",  ""+11);
 			imp_ml.setProperty("metaBlueSky",         ""+12);
-			(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_ml);			
+			JP46_Reader_camera.encodeProperiesToInfo(imp_ml);			
 			FileSaver fs=new FileSaver(imp_ml);
 			fs.saveAsTiff(file_path);
 			System.out.println("intersceneExport(): saved "+file_path);

src/main/java/com/elphel/imagej/tileprocessor/TwoQuadCLT.java

@@ -6220,7 +6220,7 @@ if (debugLevel > -100) return true; // temporarily !
 		}
 		imp_ml.setProperty("comment_disparityRadiusAux",  "Side of the square where 4 main camera subcameras are located (mm). Disparity is specified for the main camera");
 
-		(new JP46_Reader_camera(false)).encodeProperiesToInfo(imp_ml);
+		JP46_Reader_camera.encodeProperiesToInfo(imp_ml);
 		imp_ml.getProcessor().resetMinAndMax();
 		if (show ) {
 			imp_ml.show();

src/main/java/com/elphel/imagej/vegetation/VegetationSegment.java

+package com.elphel.imagej.vegetation;
+
+import java.awt.Rectangle;
+
+public class VegetationSegment {
+	public Rectangle   woi;
+	public double []   scene_offsets;
+	public double [][] tva;
+	public VegetationSegment(
+			Rectangle   woi,
+			double []   scene_offsets,
+			double [][]  tva) {
+		this.woi = woi;
+		this.scene_offsets = scene_offsets;
+		this.tva =  tva;
+	}
+}